I am trying to reconstruct cell nuclei from a large stack of nervous tissue and I have obtained a segmentation using ilastik. I imported the original stack of images into TrakEM2 and also imported the segmented images through “import labels as area lists.” However, the area list encompasses all objects (nuclei), and I would like to make each object its own separate entity. Is it possible to automate a process that labels each nucleus such that each nucleus has an individual number?
Open the segmented nuclei as a regular ImageJ stack, run standard commands to segment them (particularly easy if they are not contacting each other; for example with “Find particles”) and then assign a different label (value of 1, 2, 3, 4 … to the pixels of each by iterating all rois and filling them with those values) and only then save that stack and import it into TrakEM2 as area lists. Use a 16-bit or 32-bit stack, depending on how many nuclei there are.